Ovarian cancer is the third most common gynecologic malignancy in the United States. The purpose of this study is to evaluate the effectiveness of high dose chemotherapy with autologous stem cell transplantation for patients with ovarian cancer. Another objective of this study will be to determine what is the highest dose of topotecan that can be tolerated when combined with paclitaxel, carboplatin, topotecan, etoposide and thiotepa. The study is designed to determine the maximal tolerated dose (MTD) of topotecan combined with a fixed dose of etoposide as a component of a multi-cycle high dose chemotherapy regimen supported by peripheral blood progenitor cells. This study will evaluate the response, time to progression, disease free survival and overall survival of ovarian cancer patients with persistent, refractory, or recurrent disease. It will evaluate the feasibility and toxicity of this treatment regimen. This study will also characterize the pharmacokinetic behavior of escalating doses of topotecan during a 36 hour continuous infusion.